12-48145125-G-A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_000289.6(PFKM):c.2087G>A(p.Arg696His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 1,613,446 control chromosomes in the GnomAD database, including 185 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R696C) has been classified as Uncertain significance.
Frequency
Consequence
NM_000289.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PFKM | NM_000289.6 | c.2087G>A | p.Arg696His | missense_variant | 21/23 | ENST00000359794.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PFKM | ENST00000359794.11 | c.2087G>A | p.Arg696His | missense_variant | 21/23 | 1 | NM_000289.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0105 AC: 1596AN: 152210Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00969 AC: 2436AN: 251424Hom.: 20 AF XY: 0.00960 AC XY: 1305AN XY: 135874
GnomAD4 exome AF: 0.0145 AC: 21175AN: 1461118Hom.: 174 Cov.: 31 AF XY: 0.0140 AC XY: 10211AN XY: 726922
GnomAD4 genome AF: 0.0105 AC: 1597AN: 152328Hom.: 11 Cov.: 32 AF XY: 0.00954 AC XY: 711AN XY: 74494
ClinVar
Submissions by phenotype
Glycogen storage disease, type VII Benign:5
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | May 18, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Likely benign, criteria provided, single submitter | clinical testing | Counsyl | Mar 06, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 02, 2023 | - - |
not specified Benign:3
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Feb 18, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 03, 2018 | - - |
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Jan 09, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 24, 2021 | This variant is associated with the following publications: (PMID: 22133655, 7825568, 22995991, 20981092) - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | PFKM: BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at